User:Eran Hodis/Sandbox6

Introduction
The nucleosome core particle contains two copies of each histone protein (H2A, H2B, H3 and H4) and 146 basepairs (bp) of superhelical DNA wrapped around this histone octamer. It represents the first order of DNA packaging in the nucleus and as such is the principal structure that determines DNA accessibility.

The Histone Octamer
load molecule background [xffffff]; javascript "/cgi-bin/getlateststructure?1aoi"; set frank off; set echo bottom center; echo PDB ID: 1AOI; color echo black; select all; spin off; wireframe off; spacefill off; trace off; set ambient 40; set specpower 40; slab off; ribbons off; cartoons off; label off; monitor off; rotate x 5; rotate y 180; rotate z -2; zoom 110; translate y -4; select dna; color cpk; spacefill; select DNA and backbone; color violet; select protein; spacefill; color tan; select t1; wireframe off; select a1; wireframe off; move 0 360 0 0 0 0 0 0 6

background [xffffff]; javascript "/cgi-bin/getlateststructure?1aoi"; set frank off; select all; spin off; wireframe off; spacefill off; trace off; set ambient 40; set specpower 40; slab off; ribbons off; cartoons off; label off; monitor off; rotate x 5; rotate y 180; rotate z -2; zoom 110; translate y -4; select dna; color cpk; spacefill; select DNA and backbone; color violet; select protein; spacefill; color tan; select t1; wireframe off; select a1; wireframe off; delay 1; select protein; wireframe off; cartoons off; spacefill off; cartoons; spacefill; select *:a, *:e; color [x63529C]; select *:b, *:f; color green; select *:c, *:g; color [xFFF200]; select *:d, *:h; color[xFC351F]; delay 1; select dna; spacefill 300; delay .2; spacefill 250; delay .2; spacefill 200; delay .2; spacefill 150; delay .2; spacefill 100; delay .2; spacefill 50; delay .2; spacefill 25; delay .2; spacefill off; wireframe off; move 0 180 0 0 0 0 0 0 4; delay 1; move 0 180 0 0 0 0 0 0 4; Two copies of each histone protein, H2A, H2B , H3 , and H4 , are assembled into an octameric disc. Although each monomer has an N-terminal tail that projects from the histone core, the structure at left shows only a single tail from one H3 monomer.

background [xffffff]; javascript "/cgi-bin/getlateststructure?1aoi"; set frank off; select all; spin off; wireframe off; spacefill off; trace off; set ambient 40; set specpower 40; slab off; ribbons off; cartoons off; label off; monitor off; rotate x 5; rotate y 180; rotate z -2; zoom 110; translate y -4; select dna; color cpk; spacefill; select DNA and backbone; color violet; select protein; spacefill; color tan; select t1; wireframe off; select a1; wireframe off; delay 1; select protein; wireframe off; cartoons off; spacefill off; cartoons; spacefill; select *:a, *:e; color [x63529C]; select *:b, *:f; color green; select *:c, *:g; color [xFFF200]; select *:d, *:h; color[xFC351F]; delay 1; select dna; spacefill 300; delay .2; spacefill 250; delay .2; spacefill 200; delay .2; spacefill 150; delay .2; spacefill 100; delay .2; spacefill 50; delay .2; spacefill 25; delay .2; spacefill off; wireframe off; select protein; spacefill 300; delay .2; spacefill 250; delay .2; spacefill 200; delay .2; spacefill 150; delay .2; spacefill 100; delay .2; spacefill 50; delay .2; spacefill 25; delay .2; spacefill off; wireframe off; delay.5; define not_g *:c, *:a, *:e, *:b, *:f, *:h, *:d; select not_g and helix; trace 30; cartoons 350; delay .1; cartoons 325; delay .1; cartoons 300; delay .1; cartoons 275; delay .1; cartoons 250; delay .1; cartoons 200; delay .1; cartoons 175; delay .1; cartoons 150; delay .1; cartoons 125; delay .1; cartoons 100; delay .1; cartoons 75; delay .1; select not_g; cartoons 50; delay .1; cartoons 30; trace 30; delay .1; cartoons off; trace 10; delay .1; trace off; restrict 27-97:g; wireframe off; cartoons; color tan; select 26-38; color gold; select 39-45; color purple; select 46-73; color deepskyblue; select 74-78; color red; select 79-97; color [x808080]; select atomno= 5451; label off; select atomno= 5150; label Alpha 2; color label deepskyblue; select atomno= 1756; label Loop 1; select atomno= 4976; label Alpha 1; select atomno= 5374; label Alpha 3; select atomno= 5284; label Loop 2; delay 1; moveto 4.0 { -18 -999 44 179.91}   310.0 35.2 -46.93   {41.766502 99.7805 8.903} 82.66305  {0.0 0.0 0.0} 114.375595 186.82755 50.0; delay 1; move 0 -90 0 0 0 0 0 0 3; delay 1; move 0 90 0 0 0 0 0 0 3 All four histone proteins share a highly similar structural motif, the histone fold, comprising three alpha helices connected by two loops (shown here for H2A ): alpha1 -loop1 - alpha2 -loop2-alpha3